Compiling the OCTP Plugin in LAMMPS

LAMMPS LAMMPS Development
1

Hi,

I installed LAMMPS on August 29, 2024, using the following commands:

sudo apt update
sudo apt upgrade -y
sudo apt install -y cmake build-essential ccache gfortran openmpi-bin libopenmpi-dev \ libfftw3-dev libjpeg-dev libpng-dev python3-dev python3-pip \ python3 virtualenv libblas-dev liblapack-dev libhdf5-serial-dev \ hdf5-tools
cd lammps
mkdir build
cd build
cmake …/cmake
ccmake …/cmake/
make -j 4
make install

After that, I compiled OCTP as per the instructions from this (GitHub - omoultosEthTuDelft/OCTP: On-the-fly calculation of Transport Properties):

cd ∼/LAMMPS/src # Navigating to the LAMMPS source directory
git clone GitHub - omoultosEthTuDelft/OCTP: On-the-fly calculation of Transport Properties # Cloning the OCTP repository
cp ./OCTP/.cpp ./ # Copying all C++ files to the LAMMPS source directory
cp ./OCTP/.h ./ # Copying all header files to the LAMMPS source directory
make mpi # Recompiling LAMMPS to create the lmp_mpi executable

However, when I try to use the compiled compute position and fix ordern commands, I encounter the following error:

[LAPTOP-USR8SKUN:53391] *** Process received signal ***
[LAPTOP-USR8SKUN:53391] Signal: Segmentation fault (11)
[LAPTOP-USR8SKUN:53391] Signal code: Address not mapped (1)
[LAPTOP-USR8SKUN:53391] Failing at address: 0x5604fb647268
[LAPTOP-USR8SKUN:53391] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x42520)[0x7f63357cb520]
[LAPTOP-USR8SKUN:53391] [ 1] lmp(+0x671b56)[0x5604f99d3b56]
[LAPTOP-USR8SKUN:53391] [ 2] lmp(+0x1c5d28)[0x5604f9527d28]
[LAPTOP-USR8SKUN:53391] [ 3] lmp(+0x2f2972)[0x5604f9654972]
[LAPTOP-USR8SKUN:53391] [ 4] lmp(+0x27502e)[0x5604f95d702e]
[LAPTOP-USR8SKUN:53391] [ 5] lmp(+0x16eb1d)[0x5604f94d0b1d]
[LAPTOP-USR8SKUN:53391] [ 6] lmp(+0x16eede)[0x5604f94d0ede]
[LAPTOP-USR8SKUN:53391] [ 7] lmp(+0x15f061)[0x5604f94c1061]
[LAPTOP-USR8SKUN:53391] [ 8] /lib/x86_64-linux-gnu/libc.so.6(+0x29d90)[0x7f63357b2d90]
[LAPTOP-USR8SKUN:53391] [ 9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0x80)[0x7f63357b2e40]
[LAPTOP-USR8SKUN:53391] [10] lmp(+0x1607f5)[0x5604f94c27f5]
[LAPTOP-USR8SKUN:53391] *** End of error message ***

Could you please guide me on how to resolve this issue? Any suggestions would be appreciated.

Thank you!

helium.data (51.4 KB)
in.gcmc.H2.txt (437 Bytes)
log.lammps (2.5 KB)

2

This is not part of LAMMPS, so you have to contact its author about any issues you have.

The most important part it to pay attention to a) the LAMMPS version you are using and b) whether this external code was tested with that specific LAMMPS version. Some internals of LAMMPS have changed over time and thus require adjustments: 4.10. Notes for updating code written for older LAMMPS versions — LAMMPS documentation